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Detailed information for vg1020720683:

Variant ID: vg1020720683 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 20720683
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

AATAGAGACACAGAGACTGAATTGAGCATCCCTTTTCAAACAAGAGTTTACATGGGAATTTATATTTCATTTTATCATCCCGGGGCAGCTCTAGGGTGAG[C/T]
TCCTCGATCCCAGGGATAGCTGCATCAAGCCAATGGTTGATATGATGGGCAGACAACTCATGAAAAAATTGTAGTTCAAACCTAAACCTCTTCACCCAAC

Reverse complement sequence

GTTGGGTGAAGAGGTTTAGGTTTGAACTACAATTTTTTCATGAGTTGTCTGCCCATCATATCAACCATTGGCTTGATGCAGCTATCCCTGGGATCGAGGA[G/A]
CTCACCCTAGAGCTGCCCCGGGATGATAAAATGAAATATAAATTCCCATGTAAACTCTTGTTTGAAAAGGGATGCTCAATTCAGTCTCTGTGTCTCTATT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.70%	4.10%	0.55%	59.63%	NA
All Indica	2759	2.20%	1.00%	0.58%	96.23%	NA
All Japonica	1512	96.00%	0.70%	0.20%	3.11%	NA
Aus	269	43.90%	27.50%	0.74%	27.88%	NA
Indica I	595	2.90%	0.80%	0.84%	95.46%	NA
Indica II	465	1.30%	0.40%	0.43%	97.85%	NA
Indica III	913	1.00%	0.20%	0.33%	98.47%	NA
Indica Intermediate	786	3.60%	2.40%	0.76%	93.26%	NA
Temperate Japonica	767	98.30%	0.00%	0.00%	1.69%	NA
Tropical Japonica	504	93.50%	0.80%	0.40%	5.36%	NA
Japonica Intermediate	241	94.20%	2.50%	0.41%	2.90%	NA
VI/Aromatic	96	19.80%	75.00%	1.04%	4.17%	NA
Intermediate	90	42.20%	12.20%	4.44%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1020720683	C -> T	LOC_Os10g38890.1	synonymous_variant ; p.Glu94Glu; LOW	synonymous_codon	Average:30.41; most accessible tissue: Callus, score: 65.274	N	N	N	N
vg1020720683	C -> DEL	LOC_Os10g38890.1	N	frameshift_variant	Average:30.41; most accessible tissue: Callus, score: 65.274	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1020720683	NA	2.36E-15	mr1164	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	5.54E-08	mr1249	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	5.13E-29	mr1298	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	2.16E-20	mr1477	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	1.10E-46	mr1509	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	8.45E-06	NA	mr1510	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	2.16E-08	8.83E-63	mr1558	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	1.51E-20	mr1580	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	8.35E-10	mr1714	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	3.60E-26	mr1731	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	3.35E-12	mr1744	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	4.36E-29	mr1793	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	3.54E-17	mr1825	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	2.78E-11	mr1938	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	3.18E-21	mr1943	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	1.04E-16	mr1950	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	4.89E-19	mr1167_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	1.19E-47	mr1509_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	3.47E-06	1.76E-72	mr1558_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	4.79E-17	mr1578_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	6.74E-20	mr1581_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	1.99E-21	mr1698_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	1.38E-19	mr1746_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	1.32E-07	mr1819_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683	NA	5.77E-15	mr1950_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251